surface measurement

[Justin Murdock-2]

I am looking for a way to use imagej to measure the actual 3D surface area
of an object (in um2 or mm2). In my case, I need to determine the increase
in actual surface area among surfaces of increasing roughness (e.g. glass,
tiles, rocks, etc.). The images I have to work with consist of internally
calibrated z stacks acquired from a confocl microscope at 10x magnification.
I have been working with surfacej, but am still not sure if it can do this.

Thanks,

Justin

[Robert Dougherty]

I'm not sure about SurfaceJ, but SurfCharJ (see Gary Chinga's site
http://home.online.no/~gary.c/IJ/Plugins.html) can almost do it.  Let gx =
(partial z/partial x) and gy = (partial z/partial y).  The surface area
element is da = sqrt(1 + gx^2 + gy^2).  The facet orientation of part of
SurfCharJ (or Facet_orientation on
http://www.optinav.com/ImageJplugins/Facet-Orientation.htm) computes theta
from theta = atan(sqrt(gx^2 + gy^2)).  Thus, da = sqrt(1 + (tan(theta))^2).
This would be a fairly easy macro.  You'd want to compute theta, convert to
radians, evaluate the da expression, and integrate.  One of the plugins
could also be modified to compute the area directly.

Bob

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Justin Murdock
> Sent: Wednesday, September 28, 2005 9:11 AM
> To: [hidden email]
> Subject: surface measurement
>
> I am looking for a way to use imagej to measure the actual 3D surface area
> of an object (in um2 or mm2). In my case, I need to determine the increase
> in actual surface area among surfaces of increasing roughness (e.g. glass,
> tiles, rocks, etc.). The images I have to work with consist of internally
> calibrated z stacks acquired from a confocl microscope at 10x
> magnification.
> I have been working with surfacej, but am still not sure if it can do
> this.
>
> Thanks,
>
> Justin

[Justin Murdock-2]

Robert Dougherty wrote:

>I'm not sure about SurfaceJ, but SurfCharJ (see Gary Chinga's site
>http://home.online.no/~gary.c/IJ/Plugins.html) can almost do it.  Let gx =
>(partial z/partial x) and gy = (partial z/partial y).  The surface area
>element is da = sqrt(1 + gx^2 + gy^2).  The facet orientation of part of
>SurfCharJ (or Facet_orientation on
>http://www.optinav.com/ImageJplugins/Facet-Orientation.htm) computes theta
>from theta = atan(sqrt(gx^2 + gy^2)).  Thus, da = sqrt(1 + (tan(theta))^2).
>This would be a fairly easy macro.  You'd want to compute theta, convert to
>radians, evaluate the da expression, and integrate.  One of the plugins
>could also be modified to compute the area directly.
>
>Bob
>
>Robert P. Dougherty, Ph.D.
>President, OptiNav, Inc.
>Phone [phone]
>Fax [phone]
>www.optinav.com
>
>  
>
>>-----Original Message-----
>>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>Justin Murdock
>>Sent: Wednesday, September 28, 2005 9:11 AM
>>To: [hidden email]
>>Subject: surface measurement
>>
>>I am looking for a way to use imagej to measure the actual 3D surface area
>>of an object (in um2 or mm2). In my case, I need to determine the increase
>>in actual surface area among surfaces of increasing roughness (e.g. glass,
>>tiles, rocks, etc.). The images I have to work with consist of internally
>>calibrated z stacks acquired from a confocl microscope at 10x
>>magnification.
>>I have been working with surfacej, but am still not sure if it can do
>>this.
>>
>>Thanks,
>>
>>Justin
>>    
>>
>
>  
>

Thanks for your help Robert.  I have been working with your suggestions
to claclulate surface area using SurfCharj but haven't quite gotten it
yet. My programming skills are limited.  Thanks anyway.

Justin